Celem raportu było sprawdzenie wpływu wartości wyników badania krwi na śmiertelność COVID-19, więcej informacji na temat samych badań oraz ich przeprowadzania można znaleźć w tym artykule.
Raport składa się z przedstawienia danych, zbadania korelacji między smiertelnością a wynikami poszczególnych badań oraz próbą zbudowania klasyfikatora który na podstawie wyników badań na wczesnym etapie choroby będzie w stanie wskazać pacjentów z większą szansą na zgon. Analiza pokazała że największy wpływ na śmiertelność maja te badania: Lactate_dehydrogenase, X…lymphocyte, neutrophils_count, neutrophils… oraz wiek.
## [1] "reshape2" "rstatix" "caret" "lattice" "corrplot" "plotly"
## [7] "crosstalk" "tidyr" "ggplot2" "dplyr" "tibble" "openxlsx"
## [13] "readxl" "stats" "graphics" "grDevices" "utils" "datasets"
## [19] "methods" "base"
Zbiór danych składał się ze zbioru badań 375 pacjentów, przy czym każde badanie składało się z wybranych testów oraz daty wykonania badania. Dodatkowo każdy z pacjentów był opisany przez wiek, płeć, datę przyjęcia do szpitala, datę opuszczenia szpitala oraz parametr określający, czy pacjent przeżył. Podstawowe statystyki związane z konkretnymi badaniami zostały przedstawione poniżej.
| Hypersensitive_cardiac_troponinI | Min. : 1.9 | 1st Qu.: 4.4 | Median : 20.6 | Mean : 1223.2 | 3rd Qu.: 223.8 | Max. :50000.0 | NA’s :5613 |
| hemoglobin | Min. : 6.4 | 1st Qu.:113.0 | Median :125.0 | Mean :123.1 | 3rd Qu.:137.0 | Max. :178.0 | NA’s :5145 |
| Serum_chloride | Min. : 71.50 | 1st Qu.: 99.05 | Median :102.10 | Mean :103.14 | 3rd Qu.:105.65 | Max. :140.40 | NA’s :5145 |
| Prothrombin_time | Min. : 11.50 | 1st Qu.: 13.60 | Median : 14.80 | Mean : 16.68 | 3rd Qu.: 16.70 | Max. :120.00 | NA’s :5458 |
| procalcitonin | Min. : 0.020 | 1st Qu.: 0.040 | Median : 0.100 | Mean : 1.107 | 3rd Qu.: 0.405 | Max. :57.170 | NA’s :5661 |
| eosinophils… | Min. :0.000 | 1st Qu.:0.000 | Median :0.100 | Mean :0.629 | 3rd Qu.:0.800 | Max. :8.600 | NA’s :5163 |
| Interleukin_2_receptor | Min. : 61.0 | 1st Qu.: 459.5 | Median : 676.5 | Mean : 907.2 | 3rd Qu.:1155.5 | Max. :7500.0 | NA’s :5852 |
| Alkaline_phosphatase | Min. : 17.00 | 1st Qu.: 54.00 | Median : 69.50 | Mean : 82.47 | 3rd Qu.: 95.00 | Max. :620.00 | NA’s :5190 |
| albumin | Min. :13.60 | 1st Qu.:27.40 | Median :32.20 | Mean :32.01 | 3rd Qu.:36.60 | Max. :48.60 | NA’s :5186 |
| basophil… | Min. :0.00 | 1st Qu.:0.10 | Median :0.20 | Mean :0.21 | 3rd Qu.:0.30 | Max. :1.70 | NA’s :5163 |
| Interleukin_10 | Min. : 5.00 | 1st Qu.: 5.00 | Median : 5.90 | Mean : 16.07 | 3rd Qu.: 12.35 | Max. :1000.00 | NA’s :5853 |
| Total_bilirubin | Min. : 2.50 | 1st Qu.: 7.40 | Median : 10.70 | Mean : 16.70 | 3rd Qu.: 16.77 | Max. :505.70 | NA’s :5190 |
| Platelet_count | Min. : -1.0 | 1st Qu.:109.0 | Median :178.0 | Mean :184.3 | 3rd Qu.:248.0 | Max. :558.0 | NA’s :5163 |
| monocytes… | Min. : 0.300 | 1st Qu.: 2.800 | Median : 5.700 | Mean : 6.155 | 3rd Qu.: 8.600 | Max. :53.000 | NA’s :5162 |
| antithrombin | Min. : 20.00 | 1st Qu.: 74.00 | Median : 86.00 | Mean : 85.32 | 3rd Qu.: 97.00 | Max. :136.00 | NA’s :5790 |
| Interleukin_8 | Min. : 5.000 | 1st Qu.: 8.675 | Median : 16.000 | Mean : 83.088 | 3rd Qu.: 35.200 | Max. :6795.000 | NA’s :5852 |
| indirect_bilirubin | Min. : 0.100 | 1st Qu.: 3.800 | Median : 5.400 | Mean : 6.889 | 3rd Qu.: 8.000 | Max. :145.100 | NA’s :5214 |
| Red_blood_cell_distribution_width | Min. :10.60 | 1st Qu.:12.00 | Median :12.60 | Mean :13.07 | 3rd Qu.:13.70 | Max. :27.10 | NA’s :5197 |
| neutrophils… | Min. : 1.7 | 1st Qu.:65.1 | Median :82.4 | Mean :77.6 | 3rd Qu.:92.3 | Max. :98.9 | NA’s :5163 |
| total_protein | Min. :31.80 | 1st Qu.:61.00 | Median :65.90 | Mean :65.30 | 3rd Qu.:70.45 | Max. :88.70 | NA’s :5189 |
| Quantification_of_Treponema_pallidum_antibodies | Min. : 0.020 | 1st Qu.: 0.040 | Median : 0.050 | Mean : 0.132 | 3rd Qu.: 0.070 | Max. :11.950 | NA’s :5841 |
| Prothrombin_activity | Min. : 6.00 | 1st Qu.: 65.00 | Median : 81.00 | Mean : 78.55 | 3rd Qu.: 95.00 | Max. :142.00 | NA’s :5461 |
| HBsAg | Min. : 0.000 | 1st Qu.: 0.000 | Median : 0.010 | Mean : 8.306 | 3rd Qu.: 0.010 | Max. :250.000 | NA’s :5841 |
| mean_corpuscular_volume | Min. : 61.60 | 1st Qu.: 86.90 | Median : 90.10 | Mean : 90.39 | 3rd Qu.: 93.90 | Max. :118.90 | NA’s :5163 |
| hematocrit | Min. :14.50 | 1st Qu.:33.50 | Median :36.60 | Mean :36.55 | 3rd Qu.:39.90 | Max. :52.30 | NA’s :5163 |
| White_blood_cell_count | Min. : 0.13 | 1st Qu.: 4.94 | Median : 7.72 | Mean : 15.60 | 3rd Qu.: 12.72 | Max. :1726.60 | NA’s :4993 |
| Tumor_necrosis_factorα | Min. : 4.00 | 1st Qu.: 6.70 | Median : 8.60 | Mean : 11.58 | 3rd Qu.: 11.50 | Max. :168.00 | NA’s :5852 |
| mean_corpuscular_hemoglobin_concentration | Min. :286.0 | 1st Qu.:333.0 | Median :343.0 | Mean :342.8 | 3rd Qu.:350.0 | Max. :514.0 | NA’s :5163 |
| fibrinogen | Min. : 0.500 | 1st Qu.: 3.050 | Median : 4.120 | Mean : 4.294 | 3rd Qu.: 5.480 | Max. :10.780 | NA’s :5554 |
| Interleukin_1β | Min. : 5.00 | 1st Qu.: 5.00 | Median : 5.00 | Mean : 6.51 | 3rd Qu.: 5.00 | Max. :88.50 | NA’s :5852 |
| Urea | Min. : 0.800 | 1st Qu.: 4.000 | Median : 5.985 | Mean : 9.589 | 3rd Qu.:11.400 | Max. :68.400 | NA’s :5184 |
| lymphocyte_count | Min. : 0.000 | 1st Qu.: 0.460 | Median : 0.800 | Mean : 1.017 | 3rd Qu.: 1.310 | Max. :52.420 | NA’s :5163 |
| PH_value | Min. :5.000 | 1st Qu.:6.000 | Median :6.500 | Mean :6.484 | 3rd Qu.:7.294 | Max. :7.565 | NA’s :5736 |
| Red_blood_cell_count | Min. : 0.100 | 1st Qu.: 3.680 | Median : 4.140 | Mean : 9.288 | 3rd Qu.: 4.650 | Max. :749.500 | NA’s :4993 |
| Eosinophil_count | Min. :0.000 | 1st Qu.:0.000 | Median :0.010 | Mean :0.039 | 3rd Qu.:0.060 | Max. :0.490 | NA’s :5163 |
| Corrected_calcium | Min. :1.650 | 1st Qu.:2.270 | Median :2.360 | Mean :2.355 | 3rd Qu.:2.440 | Max. :2.790 | NA’s :5206 |
| Serum_potassium | Min. : 2.760 | 1st Qu.: 3.950 | Median : 4.410 | Mean : 4.509 | 3rd Qu.: 4.870 | Max. :12.800 | NA’s :5140 |
| glucose | Min. : 1.000 | 1st Qu.: 5.550 | Median : 6.990 | Mean : 8.889 | 3rd Qu.:10.260 | Max. :43.010 | NA’s :5345 |
| neutrophils_count | Min. : 0.06 | 1st Qu.: 3.09 | Median : 5.85 | Mean : 7.81 | 3rd Qu.:10.95 | Max. :33.88 | NA’s :5163 |
| Direct_bilirubin | Min. : 1.600 | 1st Qu.: 3.225 | Median : 4.800 | Mean : 9.887 | 3rd Qu.: 8.275 | Max. :360.600 | NA’s :5190 |
| Mean_platelet_volume | Min. : 8.50 | 1st Qu.:10.10 | Median :10.80 | Mean :10.91 | 3rd Qu.:11.50 | Max. :15.00 | NA’s :5258 |
| ferritin | Min. : 17.8 | 1st Qu.: 377.2 | Median : 711.0 | Mean : 1379.1 | 3rd Qu.: 1425.2 | Max. :50000.0 | NA’s :5837 |
| RBC_distribution_width_SD | Min. : 31.30 | 1st Qu.: 38.50 | Median : 40.90 | Mean : 42.44 | 3rd Qu.: 44.70 | Max. :113.30 | NA’s :5197 |
| Thrombin_time | Min. : 13.00 | 1st Qu.: 15.60 | Median : 16.80 | Mean : 18.17 | 3rd Qu.: 18.38 | Max. :161.90 | NA’s :5554 |
| X…lymphocyte | Min. : 0.000 | 1st Qu.: 3.925 | Median :11.450 | Mean :15.392 | 3rd Qu.:24.975 | Max. :60.000 | NA’s :5162 |
| HCV_antibody_quantification | Min. :0.020 | 1st Qu.:0.040 | Median :0.060 | Mean :0.117 | 3rd Qu.:0.090 | Max. :2.090 | NA’s :5841 |
| D.D_dimer | Min. : 0.210 | 1st Qu.: 0.603 | Median : 2.155 | Mean : 7.943 | 3rd Qu.:21.000 | Max. :60.000 | NA’s :5490 |
| Total_cholesterol | Min. :0.100 | 1st Qu.:3.010 | Median :3.630 | Mean :3.689 | 3rd Qu.:4.265 | Max. :7.300 | NA’s :5189 |
| aspartate_aminotransferase | Min. : 6.00 | 1st Qu.: 19.50 | Median : 27.00 | Mean : 46.53 | 3rd Qu.: 42.00 | Max. :1858.00 | NA’s :5185 |
| Uric_acid | Min. : 43.0 | 1st Qu.: 183.2 | Median : 243.7 | Mean : 276.1 | 3rd Qu.: 333.8 | Max. :1176.0 | NA’s :5186 |
| HCO3. | Min. : 6.30 | 1st Qu.:21.00 | Median :23.50 | Mean :23.14 | 3rd Qu.:25.90 | Max. :36.30 | NA’s :5186 |
| calcium | Min. :1.170 | 1st Qu.:1.980 | Median :2.080 | Mean :2.078 | 3rd Qu.:2.190 | Max. :2.620 | NA’s :5141 |
| Amino.terminal_brain_natriuretic_peptide_precursor.NT.proBNP. | Min. : 5 | 1st Qu.: 150 | Median : 585 | Mean : 3669 | 3rd Qu.: 2625 | Max. :70000 | NA’s :5645 |
| Lactate_dehydrogenase | Min. : 110.0 | 1st Qu.: 218.0 | Median : 340.0 | Mean : 474.2 | 3rd Qu.: 601.8 | Max. :1867.0 | NA’s :5186 |
| platelet_large_cell_ratio | Min. :11.20 | 1st Qu.:25.60 | Median :30.90 | Mean :31.77 | 3rd Qu.:37.20 | Max. :62.20 | NA’s :5258 |
| Interleukin_6 | Min. : 1.500 | 1st Qu.: 4.772 | Median : 19.265 | Mean : 112.308 | 3rd Qu.: 60.167 | Max. :5000.000 | NA’s :5848 |
| Fibrin_degradation_products | Min. : 4.00 | 1st Qu.: 4.00 | Median : 17.90 | Mean : 61.35 | 3rd Qu.:150.00 | Max. :190.80 | NA’s :5790 |
| monocytes_count | Min. : 0.010 | 1st Qu.: 0.270 | Median : 0.410 | Mean : 0.526 | 3rd Qu.: 0.580 | Max. :39.920 | NA’s :5163 |
| PLT_distribution_width | Min. : 8.00 | 1st Qu.:11.10 | Median :12.40 | Mean :13.01 | 3rd Qu.:14.30 | Max. :25.30 | NA’s :5258 |
| globulin | Min. :10.10 | 1st Qu.:29.70 | Median :32.70 | Mean :33.24 | 3rd Qu.:36.50 | Max. :50.60 | NA’s :5190 |
| γ.glutamyl_transpeptidase | Min. : 3.00 | 1st Qu.: 22.00 | Median : 34.00 | Mean : 55.34 | 3rd Qu.: 58.00 | Max. :732.00 | NA’s :5190 |
| International_standard_ratio | Min. : 0.840 | 1st Qu.: 1.030 | Median : 1.140 | Mean : 1.313 | 3rd Qu.: 1.330 | Max. :13.480 | NA’s :5461 |
| basophil_count… | Min. :0.000 | 1st Qu.:0.010 | Median :0.010 | Mean :0.017 | 3rd Qu.:0.020 | Max. :0.120 | NA’s :5163 |
| X2019.nCoV_nucleic_acid_detection | Min. :-1 | 1st Qu.:-1 | Median :-1 | Mean :-1 | 3rd Qu.:-1 | Max. :-1 | NA’s :5619 |
| mean_corpuscular_hemoglobin | Min. :20.4 | 1st Qu.:29.7 | Median :30.9 | Mean :31.0 | 3rd Qu.:32.2 | Max. :50.8 | NA’s :5163 |
| Activation_of_partial_thromboplastin_time | Min. : 21.80 | 1st Qu.: 35.30 | Median : 39.20 | Mean : 41.52 | 3rd Qu.: 44.12 | Max. :144.00 | NA’s :5552 |
| High_sensitivity_C.reactive_protein | Min. : 0.10 | 1st Qu.: 5.70 | Median : 51.50 | Mean : 76.24 | 3rd Qu.:118.50 | Max. :320.00 | NA’s :5383 |
| HIV_antibody_quantification | Min. :0.05 | 1st Qu.:0.07 | Median :0.09 | Mean :0.10 | 3rd Qu.:0.11 | Max. :0.27 | NA’s :5842 |
| serum_sodium | Min. :115.4 | 1st Qu.:137.7 | Median :140.4 | Mean :141.6 | 3rd Qu.:143.5 | Max. :179.7 | NA’s :5145 |
| thrombocytocrit | Min. :0.010 | 1st Qu.:0.150 | Median :0.210 | Mean :0.212 | 3rd Qu.:0.270 | Max. :0.510 | NA’s :5258 |
| ESR | Min. : 1.00 | 1st Qu.: 14.00 | Median : 28.00 | Mean : 33.69 | 3rd Qu.: 45.50 | Max. :110.00 | NA’s :5737 |
| glutamic.pyruvic_transaminase | Min. : 5.00 | 1st Qu.: 16.00 | Median : 24.00 | Mean : 38.86 | 3rd Qu.: 41.00 | Max. :1600.00 | NA’s :5189 |
| eGFR | Min. : 2.00 | 1st Qu.: 63.58 | Median : 87.90 | Mean : 81.56 | 3rd Qu.:103.97 | Max. :224.00 | NA’s :5184 |
| creatinine | Min. : 11.00 | 1st Qu.: 58.00 | Median : 76.00 | Mean : 109.93 | 3rd Qu.: 98.25 | Max. :1497.00 | NA’s :5184 |
Zbiór danych zawiera informacje o 151 kobietach oraz 224 mężczyznach; 174 pacjentów zmarło a 201 przeżyło. Poniższe wykresy pokazują porównania liczby pacjentów w zależnoci od płci, grupy wiekowej oraz śmiertelności.
Analizując wykres Wyk.3, mogłoby się wydawać, że śmiertelność wśród kobiet jest zauważalnie mniejsza niż wśród mężczyzn ale fakt ten wynika raczej z tego że wśród pacjentów w wieku 50+ więkość stanowią mężczyźni (co pokazuje wykres Wyk.2) a właśnie dla wieku 50+ śmiertelność drastycznie rośnie (co pokazuje wykres Wyk.3). Podsumowując ze względu na nierówne rozłożenie płci pacjentów wśród grup wiekowych nie będę wykorzystywał tego parametru w dalszej analizie. Należy zwrócić uwagę wykres Wyk.3 wskazuje, że wiek pacjenta ma ogromny wpływ na to, czy pacjentowi uda się przeżyć.
Poniższy wykres pozwala porównać historię wyników wybranych badań dla wybranego pacjenta w czasie.